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Update slurm_submit to capture job ID #135

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Update slurm_submit to capture job ID #135

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630a837
Update slurm_submit to capture job ID
bio-boris Sep 9, 2025
fe50b25
Update slurm_submit with PATH check comment
bio-boris Sep 9, 2025
f12bcd3
Update slurm_checkjob with PATH instructions
bio-boris Sep 9, 2025
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2 changes: 1 addition & 1 deletion scripts/slurm_checkjob
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
# Wraper script for slurm job check
# Args are the Job ID
# Returns back Running, Finished, Pending or Unknown
#
# Ensure that slurm_submit and slurm_checkjob are in the PATH . ~/.local_settings may need to be updated
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Copilot AI Sep 9, 2025

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There's an extra space after the # character - should be '# Ensure' instead of '# Ensure' for consistency with other comments.

Suggested change
# Ensure that slurm_submit and slurm_checkjob are in the PATH . ~/.local_settings may need to be updated
# Ensure that slurm_submit and slurm_checkjob are in the PATH . ~/.local_settings may need to be updated

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JS=$(squeue -j $1 -o %t --noheader)

if [ -z "$JS" ] ; then
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6 changes: 5 additions & 1 deletion scripts/slurm_submit
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Expand Up @@ -3,9 +3,13 @@
# Wrapper script for Slurm batch submit
# Args are submit script, outputfile, and error file
# Return the job id via stdout
# Ensure that slurm_submit and slurm_checkjob are in the PATH . ~/.local_settings may need to be updated
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Copilot AI Sep 9, 2025

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There's an extra space in 'that slurm_submit' - should be 'that slurm_submit' with only one space.

Suggested change
# Ensure that slurm_submit and slurm_checkjob are in the PATH . ~/.local_settings may need to be updated
# Ensure that slurm_submit and slurm_checkjob are in the PATH . ~/.local_settings may need to be updated

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module purge
PATH=/usr/common/software/bin:/usr/common/mss/bin:/usr/common/nsg/bin:/opt/ovis/bin:/opt/ovis/sbin:/usr/local/bin:/usr/bin:/bin:/usr/lib/mit/bin:/usr/lib/mit/sbin
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I generally don't think paths should be hardcoded in scripts, but it seems unlikely this script is ever going to be used for anything other than hipmer so it's probably fine


SUBMIT=$1
LOGFILE=$2
ERRFILE=$3

sbatch -o $LOGFILE -e $ERRFILE $SUBMIT
sbatch -o $LOGFILE -e $ERRFILE $SUBMIT|sed 's/Submitted batch job //'
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Copilot AI Sep 9, 2025

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The sed command assumes sbatch will always output 'Submitted batch job ' prefix. Consider adding error handling to verify the command succeeded and the output format is as expected before parsing.

Suggested change
sbatch -o $LOGFILE -e $ERRFILE $SUBMIT|sed 's/Submitted batch job //'
# Submit the job and capture output
SBATCH_OUTPUT=$(sbatch -o "$LOGFILE" -e "$ERRFILE" "$SUBMIT")
SBATCH_EXIT=$?
# Check if sbatch succeeded
if [ $SBATCH_EXIT -ne 0 ]; then
echo "Error: sbatch failed with exit code $SBATCH_EXIT" >&2
echo "$SBATCH_OUTPUT" >&2
exit $SBATCH_EXIT
fi
# Extract job ID from output
if [[ "$SBATCH_OUTPUT" =~ ^Submitted\ batch\ job\ ([0-9]+) ]]; then
echo "${BASH_REMATCH[1]}"
else
echo "Error: Unexpected sbatch output format:" >&2
echo "$SBATCH_OUTPUT" >&2
exit 1
fi

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